Error: Unable to access jarfile None

[maojn]

Hi,
I got the following error when using the test data:
$ hint pre -d /fdb/hint/testData/TestSub_1.fq.gz,/fdb/hint/testData/TestSub_2.fq.gz
-i /fdb/hint/bwaIndex/hg19/hg19.fa
--refdir /fdb/hint/references/hg19
--informat fastq
--outformat juicer
-g hg19
-n test1
-o /data/apptest2/test1out
--samtoolspath /usr/local/apps/samtools/1.9/bin/samtools
-p 4
--pairtoolspath /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools
-a /usr/local/Anaconda/envs_app/hint/2.2.7/bin/bwa
…
...
/usr/local/apps/samtools/1.9/bin/samtools view -h /data/apptest2/test1out/test1.bam | /usr/local/Anaconda/envs_app/hint/2.2.7/
bin/pairtools parse -c /fdb/hint/references/hg19/hg19.len -o /data/apptest2/test1out/test1.pairsam.gz --nproc-in 4 --nproc-out
4 --assembly hg19
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools sort -o /data/apptest2/test1out/test1.sorted.pairsam.gz --memory 20G --c
ompress-program gzip --nproc-in 4 --nproc-out 4 --tmpdir /data/apptest2/test1out/tmp /data/apptest2/test1out/test1.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 --chrom-subset /fdb/hint/references/hg
19/hg19.len -o /data/apptest2/test1out/test1_valid.sorted.pairsam.gz '(pair_type == "UU") or (pair_type == "UR") or (pair_type
== "RU")' /data/apptest2/test1out/test1.sorted.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 -o /data/apptest2/test1out/test1_chime
ric.sorted.pairsam.gz '(pair_type == "NR") or (pair_type == "CC") or (pair_type == "MR")' /data/apptest2/test1out/test1.sorted
.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools dedup --nproc-in 4 --nproc-out 4 --output /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz /data/apptest2/test1out/test1_valid.sorted.pairsam.gz
/usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools split --nproc-in 4 --nproc-out 4 --output-pairs /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz
pairix -f /data/apptest2/test1out/test1_merged_valid.pairs.gz
java -jar None pre -n /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1.hic hg19
Error: Unable to access jarfile None
java -jar None addNorm -d -w 5000 -F /data/apptest2/test1out/test1.hic
Error: Unable to access jarfile None

$ which java
/usr/local/Java/jdk1.8.0_11/bin/java

I would really appreciate if someone can help with this.

Regards,

Jean

[maojn]

The instruction didn't include the flag for juicer. Problem solved once it's included.